Contacts of the helix formed by residues 199 - 217 (chain E) in PDB entry 2CNW
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 199 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248B ASP* 2.8 47.8 + - - +
272B VAL 5.2 0.4 + - - -
273B SER* 5.4 2.8 - - - +
1001B GDP 4.6 1.6 + - - -
196E LEU* 3.1 21.8 + - + +
197E HIS 3.2 0.4 - - - -
198E THR* 1.3 91.6 - - - +
200E HIS* 1.3 66.3 + - - +
201E ASN* 3.2 11.4 - - - +
202E LEU* 2.8 39.5 + - + +
203E MET* 3.1 13.3 + - - +
3001E 5GP 4.8 9.1 + - - -
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Residues in contact with HIS 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197E HIS 5.5 0.7 - - - -
198E THR 3.7 5.1 + - - -
199E LYS* 1.3 71.4 - - - +
201E ASN* 1.3 56.7 + - - +
203E MET* 3.1 13.5 + - + +
204E GLU* 2.9 66.8 + - + +
207E LYS* 4.9 3.8 + - - -
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Residues in contact with ASN 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E LYS* 3.8 18.7 - - - +
200E HIS* 1.3 79.5 + - - +
202E LEU* 1.3 74.6 + - - +
204E GLU* 3.5 8.2 + - - +
205E GLU* 3.0 25.1 + - - +
3001E 5GP 4.6 19.5 + - - -
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Residues in contact with LEU 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E ARG* 2.8 50.4 + - + +
196E LEU 4.9 2.0 - - - +
199E LYS* 2.8 38.9 + - + +
201E ASN* 1.3 85.1 - - - +
203E MET* 1.3 61.3 + - - +
205E GLU* 3.4 8.6 - - - +
206E LEU 3.1 12.5 + - - -
3001E 5GP 3.5 72.7 - - + +
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Residues in contact with MET 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E ARG* 4.0 21.5 - - - -
196E LEU 4.3 0.7 - - - +
197E HIS* 3.8 34.3 - - + +
199E LYS 3.1 13.3 + - - +
200E HIS* 3.1 15.7 + - + +
202E LEU* 1.3 75.6 - - - +
204E GLU* 1.3 60.2 + - + +
206E LEU* 3.2 8.4 + - + +
207E LYS* 3.0 31.7 + - - +
242E LYS* 3.7 26.9 - - + +
243E PHE* 3.5 32.3 - - + -
246E ALA* 3.8 19.8 - - + +
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Residues in contact with GLU 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E HIS* 2.9 49.1 + - + +
201E ASN* 3.7 7.4 - - - +
203E MET* 1.3 72.7 - - - +
205E GLU* 1.3 61.1 + - - +
207E LYS* 2.7 45.1 + - - +
208E LYS* 2.9 31.0 + - - +
211E ARG* 4.2 11.3 + - - -
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Residues in contact with GLU 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E ASP* 6.0 0.4 - - - +
169E PRO* 3.8 29.1 - - + +
170E ALA* 6.6 0.2 - - + -
193E ALA* 5.4 0.9 - - - +
195E ARG* 2.3 36.6 + - - +
201E ASN 3.0 15.5 + - - +
202E LEU* 3.4 15.9 - - + +
204E GLU* 1.3 77.1 - - - +
206E LEU* 1.3 56.8 + - - +
208E LYS* 3.1 30.6 - - + +
209E VAL* 3.1 11.6 + - + +
3001E 5GP 2.4 40.7 + - - +
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Residues in contact with LEU 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E LEU* 4.8 7.2 - - + +
108E VAL* 3.7 21.8 - - + -
192E THR* 3.6 35.2 - - + +
195E ARG* 3.8 16.6 - - - +
202E LEU 3.1 11.6 + - - +
203E MET* 3.5 13.2 - - + +
204E GLU 3.2 0.4 - - - -
205E GLU* 1.3 75.2 - - - +
207E LYS* 1.3 65.3 + - - +
209E VAL* 3.3 9.8 + - + +
210E LYS* 3.1 21.7 + - - +
243E PHE* 3.7 37.0 - - + -
246E ALA* 5.6 0.4 - - + -
247E VAL* 4.1 16.8 - - + +
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Residues in contact with LYS 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E HIS* 4.9 4.2 + - - -
203E MET* 3.0 17.8 + - - +
204E GLU* 2.7 43.7 + - - +
206E LEU* 1.3 75.9 - - - +
208E LYS* 1.3 57.3 + - - +
210E LYS* 3.3 5.3 + - - +
211E ARG* 2.9 47.8 + - - +
245E GLU* 4.8 10.3 + - - -
246E ALA* 3.4 39.3 - - - +
247E VAL* 4.1 8.2 - - + +
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Residues in contact with LYS 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E ASP* 3.6 26.8 + - - -
170E ALA* 3.8 19.9 - - + +
204E GLU 2.9 13.8 + - - +
205E GLU* 3.1 20.6 + - + +
207E LYS* 1.3 74.3 - - - +
209E VAL* 1.3 57.3 + - - +
211E ARG* 3.3 28.1 + - - +
212E ALA* 2.9 28.4 + - - +
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Residues in contact with VAL 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E LEU* 4.2 22.0 - - + -
169E PRO* 4.1 17.7 - - + +
170E ALA* 3.9 25.1 - - + +
173E ALA* 3.7 23.6 - - + -
190E VAL* 4.3 4.9 - - + -
192E THR* 4.9 6.3 - - + -
195E ARG* 6.0 2.2 - - - +
205E GLU* 3.1 16.0 + - + +
206E LEU* 3.3 17.7 + - + +
208E LYS* 1.3 70.8 - - - +
210E LYS* 1.3 62.3 + - - +
212E ALA* 3.2 2.9 + - - +
213E ILE* 2.9 35.8 + - + +
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Residues in contact with LYS 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E LEU* 4.1 12.9 - - + +
206E LEU 3.1 10.4 + - - +
207E LYS* 3.5 10.8 - - - +
208E LYS 3.3 0.2 - - - -
209E VAL* 1.3 79.1 - - - +
211E ARG* 1.3 61.7 + - + +
213E ILE* 3.4 8.4 + - - +
214E ALA* 3.2 19.8 + - - +
221E PRO* 3.7 30.9 - - + +
224E VAL* 4.8 5.1 - - + +
246E ALA 5.6 0.2 - - - +
247E VAL* 2.8 47.8 + - + +
248E GLY* 4.9 1.4 + - - -
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Residues in contact with ARG 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E GLU* 4.2 12.3 + - - +
207E LYS* 2.9 47.8 + - - +
208E LYS* 3.4 37.7 - - - +
209E VAL 3.2 0.2 - - - -
210E LYS* 1.3 73.2 - - + +
212E ALA* 1.3 56.9 - - - +
214E ALA* 3.0 9.0 + - - +
215E LYS* 2.8 35.3 + - - +
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Residues in contact with ALA 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E ALA* 3.1 37.7 - - + +
173E ALA* 4.7 0.9 - - + -
174E TYR* 3.6 24.4 - - + +
208E LYS 2.9 14.0 + - - +
209E VAL 3.3 8.7 - - - +
211E ARG* 1.3 75.0 - - - +
213E ILE* 1.3 64.1 + - - +
215E LYS* 3.5 7.4 + - - +
216E ALA* 3.4 15.2 + - - +
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Residues in contact with ILE 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E VAL* 3.7 25.6 - - + -
106E LEU* 4.2 17.5 - - + -
173E ALA* 4.1 10.5 - - + -
177E VAL* 3.9 21.2 - - + +
190E VAL* 4.0 15.0 - - + -
209E VAL* 2.9 23.0 + - + +
210E LYS* 3.5 8.3 - - - +
211E ARG 3.1 0.4 - - - -
212E ALA* 1.3 76.6 - - - +
214E ALA* 1.3 56.1 + - - +
216E ALA* 3.1 6.4 + - - +
217E ASP* 3.0 25.1 + - - +
220E GLU* 3.6 12.8 - - + -
221E PRO* 3.5 35.4 - - + -
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Residues in contact with ALA 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210E LYS 3.2 10.0 + - - +
211E ARG* 3.0 11.7 + - - +
213E ILE* 1.3 70.7 - - - +
215E LYS* 1.3 66.0 + - - +
216E ALA 3.0 3.1 + - - -
217E ASP 3.1 14.3 + - - -
218E PRO* 3.1 27.3 - - + +
220E GLU 3.4 18.5 + - - +
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Residues in contact with LYS 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174E TYR* 3.8 29.3 + - + -
211E ARG 2.8 19.2 + - - +
212E ALA* 3.6 10.8 - - - +
213E ILE 3.3 0.2 - - - -
214E ALA* 1.3 73.2 - - - +
216E ALA* 1.3 58.7 + - - +
218E PRO* 5.3 1.6 - - - +
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Residues in contact with ALA 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174E TYR* 3.7 31.0 - - + +
177E VAL* 3.6 27.4 - - + -
178E GLN* 3.6 12.0 - - - +
181E LYS* 2.7 31.7 + - - -
212E ALA 3.4 2.6 + - - +
213E ILE 3.1 5.2 + - - +
214E ALA 3.0 0.6 - - - -
215E LYS* 1.3 79.1 - - - +
217E ASP* 1.3 58.1 + - - +
218E PRO* 4.3 3.5 - - - +
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Residues in contact with ASP 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E ARG* 3.6 22.6 + - - -
177E VAL* 3.7 17.5 - - + -
180E MET* 4.3 5.0 - - - +
181E LYS* 4.0 10.8 - - + +
213E ILE 3.0 4.6 + - - -
214E ALA* 3.1 7.1 + - - +
216E ALA* 1.3 79.5 - - - +
218E PRO* 1.4 63.8 - - - +
219E GLU* 2.9 13.3 + - - +
220E GLU* 2.7 58.6 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il